1YXH

Crystal structure of a novel phospholipase A2 from Naja naja sagittifera with a strong anticoagulant activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a novel phospholipase A(2) from Naja naja sagittifera with a strong anticoagulant activity

Jabeen, T.Singh, N.Singh, R.K.Ethayathulla, A.S.Sharma, S.Srinivasan, A.Singh, T.P.

(2005) Toxicon 46: 865-875

  • DOI: 10.1016/j.toxicon.2005.08.008

  • PubMed Abstract: 
  • This is the first PLA(2) crystal structure from group I that shows a strong anticoagulant property. The monomeric PLA(2) was purified from the venom of Naja naja sagittifera (Indian cobra). Its amino acid sequence has been determined using cDNA techn ...

    This is the first PLA(2) crystal structure from group I that shows a strong anticoagulant property. The monomeric PLA(2) was purified from the venom of Naja naja sagittifera (Indian cobra). Its amino acid sequence has been determined using cDNA technique. The amino acid sequence of sPLA(2) contains three positively charged and two negatively charged residues in the segment 54-71 (numbering scheme of sPLA(2)) thus giving this region an overall cationic amphiphilic surface. This suggested the presence of an anticoagulant activity in sPLA(2). The enzyme was crystallized using hanging drop vapour diffusion method in the presence of calcium chloride. The crystals belong to space group P4(1) with cell dimensions of a=b=42.0A, c=65.9A. The X-ray crystal structure was determined at 1.8A resolution using molecular replacement method and refined to an R value of 0.179 for 10,023 reflections. The overall scaffolding of sPLA(2) is essentially similar to those observed for other group I PLA(2)s. However, the conformations of various surface loops were found to be significantly different. The most significant observation pertains to the anticoagulant loop in which both the acidic residues are engaged in intramolecular interactions whereas all the three basic residues are free to interact with other molecules. This makes the sPLA(2) a potentially strong anticoagulating molecule.


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phospholipase A2
A
126Naja sagittiferaMutation(s): 0 
EC: 3.1.1.4
Find proteins for Q6T179 (Naja sagittifera)
Go to UniProtKB:  Q6T179
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.195 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 42.817α = 90.00
b = 42.817β = 90.00
c = 65.994γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance